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Iddo

Music: Bill Evans Waltz for Debbie

This week began rather  hectically for me. Time to chill with this Jazz classic.

On Molecular Viewers, or why I voted for RasMol

Beware the temptation to use the 45 and 120 degree angle pink and yellow light source, in combination with shiny plastic B-splines, which would make your protein model look like brothel decor

Happy Birthday Linux

March 14 is also the anniversary of the release of Linux kernel 1.0, with all of its 176,250 lines of code. The current 2.6.28 has  crossed the 10,000,000 threshold. Tux should have a birthday Pi…. but here is some other Tux confectionery:

A very loose and circular association to π (Pi) Day

Happy Pi (π) Day! Americans write dates in the MM/DD/YYYY format instead of the DD/MM/YYYY format used by the rest of the world.  Usually a rather painful and confusing format if you did not grow up with it, causing checks to bounce and leases to expire for those who recently moved to the US, but […]

Baby it’s cold outside

Most of the Earth’s surface is colder than the inside of your refrigerator. Deep sea temperatures are almost universally 2-4C. That’s already 73%  of the Earth’s surface. Then add to that the  polar regions, mountain ranges and permafrost and you have about 85% of the Earth’s surface constantly at refrigerator or freezer temperatures. While there […]

Mad Scientist

From Abstruse Goose

Music: In Your Darkest Hour

The first time I heard Charlie Musselwhite was on KSDS 88.3, San Diego’s jazz radio station and one for the finest jazz & blues stations I know. I was driving, it was late night and raining, and I was dead tired; the perfect setting for some blues. They played Musselwhite’s jumpy “Both Sides of the […]

Not dead, overloaded

When the Moon is in the Seventh House, and Jupiter aligns with Mars, a bunch of people gather for their “Bioinformaticians anonymous” group therapy. There they metaphorically gather, commiserating about how bioinformatics is dead (or was it bioinformaticians?), just smells funny or suffers from identity theft, probably because it got drunk at the last ISMB, […]

Post-apres-next generation sequencing

<RANT> OK, I don’t like the term “next generation sequencing”. It is a relative term, points at a changing target, and therefore inexact. What is the “this-generation sequencing”? Sanger? 454 used to be “next generation”, but now 454 sequencing went from 100bp to 600bp per read, making it qualitatively different.. so “post-next generation sequencing”? If […]

Searching for Life on Earth

But if you know what life is worth, You will look for yours on Earth — Bob Marley – “Is there life on Earth?” – “Well, duh.” – “I mean, is there another kind of life on Earth?” – “WTF?” – “You know… there could be these bugs that, like, they’re all around us and […]

Thickfreakness

I have been traveling to Ohio a bit recently… one of my favorite bands (a duo really) comes from Akron, OH. The Black Keys. First song of them I heard was this one, Thickfreaknes; still one of my favorites.

Ten years of coding with the snake

Biopython is entering its 10th year; the unofficial birthday is on September, since that is when the mailing list started: September 1999. I stumbled onto that list mid-September, 1999. I believe the Python version was 1.5, I was still working on SGI Irix, and I was an 0.3 PhD candidate. Today I am coding with […]

Metagenomes as a diagnostic tool?

Can we learn about an environment by looking at the bacteria living in it? Can we sequence a metagenome, and then say: ”according to the active genes in this water sample it appears to be too rich in metal ions / sewage products / other pollutants” ? In the foreseeable future could we sequence a […]

Blog for Darwin: on Mass Extinctions

Happy Darwin Day! If you are reading this then you probably do not need an introduction to Charles Darwin, the importance of his work, how his theory of evolution by natural selection shaped modern Biology. Or if you do, I bet there are plenty of posts in today’s blogswarm that will address this. There is […]

Metagenomics Metadata and Metaanalysis

I am a co-organizer of this… see for yourself. Cutting edge metagenomics research, discussion of standards applications to genomics and metagenomics, all in beautiful Stockholm this summer. If you are coming to ISMB/ECCB 2009, consider coming to the M3 SIG. Link to announcement 1-page poster, because you really want to tack this to your departmental […]